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jotech / gapseq

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
GNU General Public License v3.0
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network complementarity and sbml #62

Closed ntromas closed 3 years ago

ntromas commented 3 years ago

Hi,

First of all, thanks a lot for this super cool pipeline! We have isolated colonies from environment and we sequenced them. We never cultivated them. Is it possible to compare their metabolic network (to highlight cooperation or complementarity)?

Thanks!

Waschina commented 3 years ago

Hi @ntromas ! gapseq does not (maybe not yet) include functions to directly compare reconstructions. But there are some tools that can do that on the SBML-formated models, as they are also produced by gapseq. You could for instance try SMETANA (https://github.com/cdanielmachado/smetana).

ntromas commented 3 years ago

Hi, Thanks! I just tried with 2 .xml generated by gapseq, but I got this error : raise IOError("Model file was not found") OSError: Model file was not found Not sure if my models are corrects or well-formatted. Thanks for your help, Nico

Waschina commented 3 years ago

Mhh, I'm not sure why this happens. I just tried smetana with two xml files from my reconstructions, which seemed to work. Could you maybe provide more detail on the commands you are using?

ntromas commented 3 years ago

To be honest, I am very new on these pipelines. I just installed smetana, tested it (it worked) with the provided dataset. Then I run on my reconstructions (.xml files I guess): smetana M007S1_QC_C_20170808_Roseomonas_sp10_A20BQC.xml M7_QC_C_20170808_B1M.xml --global

I am probably doing something wrong...Thanks for your help!

Nico

ntromas commented 3 years ago

If that can help... Archive.zip

Waschina commented 3 years ago

That definitely helps – I will check what might be the issue here.

Silvio

Waschina commented 3 years ago

Hi Nico,

could you maybe check which version of the R-Package sybilSBML you are using? Your are right, the sbml format looks indeed different to the reconstructions that I get from gapseq, so this might be part of the issue.

You could try to install the latest version (3.1.2) of sybilSBML using the following commands:

wget https://cran.r-project.org/src/contrib/Archive/sybilSBML/sybilSBML_3.1.2.tar.gz
R CMD INSTALL sybilSBML_3.1.2.tar.gz
ntromas commented 3 years ago

Hi Silvio,

I got an older version (packageVersion("sybilSBML") : ‘3.0.1’) so I just installed the one your recommended and I am re-running gapseq. Will keep you informed! Thanks a lot for your time on this! Nico

Le mer. 7 avr. 2021 à 13:03, Silvio Waschina @.***> a écrit :

Hi Nico,

could you maybe check which version of the R-Package sybilSBML you are using? Your are right, the sbml format looks indeed different to the reconstructions that I get from gapseq, so this might be part of the issue.

You could try to install the latest version (3.1.2) of sybilSBML using the following commands:

wget https://cran.r-project.org/src/contrib/Archive/sybilSBML/sybilSBML_3.1.2.tar.gz R CMD INSTALL sybilSBML_3.1.2.tar.gz

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Nicolas Tromas PhD Université de Montréal Département de sciences biologiques Microbial Evolutionary Genomics Group-Laboratoire de Jesse Shapiro Pavillon Marie-Victorin 90 Vincent-d'Indy, Montréal, Québec, H2V 2S9 Phone: (514) 343 6111 3188 E-mail: @. @.> Researchgate: NTromasPage https://www.researchgate.net/profile/Nicolas_Tromas Web: http://www.shapirolab.ca/

ntromas commented 3 years ago

Hi Silvio, I have now the last version of the package: packageVersion("sybilSBML") [1] ‘3.1.2’

gapseq version: 1.1 3b83e9c linux-gnu

75-Ubuntu SMP Fri Feb 19 18:03:38 UTC 2021

#######################

Checking dependencies

####################### GNU Awk 5.1.0, API: 3.0 sed (GNU sed) 4.8 grep (GNU grep) 3.4 This is perl 5, version 32, subversion 0 (v5.32.0) built for x86_64-linux-thread-multi tblastn: 2.5.0+ exonerate from exonerate version 2.4.0 bedtools v2.30.0 barrnap 0.9 - rapid ribosomal RNA prediction R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" R scripting front-end version 4.0.3 (2020-10-10) git version 2.30.2

Missing dependencies: 0

#####################

Checking R packages

##################### data.table 1.14.0 stringr 1.4.0 sybil 2.1.5 getopt 1.20.3 reshape2 1.4.4 doParallel 1.0.16 foreach 1.5.1 R.utils 2.10.1 stringi 1.5.3 glpkAPI 1.3.2 BiocManager 1.30.12 Biostrings 2.58.0 jsonlite 1.7.2 CHNOSZ 1.4.0

Missing R packages: 0

##############################

Checking basic functionality

############################## Optimization test: OK Blast test: OK

Passed tests: 2/2

But with the new version, I am not able to produce a .xml (I followed the different troubleshooting you added):

Can't open M007S1_QC_C_20170808_Roseomonas_sp10_A20BQC.xml: No such file or directory. Warning messages: 1: In sybilSBML::writeSBML(mod, filename = paste0(out.id, ".xml"), : Missing Groups-plugin for libSBML. No SBML output will be written. 2: In write_gapseq_sbml(mod.out, out.id) : Writing SBML-file failed.

I probably did something wrong... Cheers,

Nico

ntromas commented 3 years ago

I think I found the issue. I followed the install_sybilSBML.sh, updating the package version. Unfortunately I am not able to make this command working: R CMD INSTALL --configure-args="--with-sbml-include=/usr/local/include/ --with-sbml-lib=/usr/local/lib/" sybilSBML_3.1.2.tar.gz Any idea? Thanks for your help&time !

jotech commented 3 years ago

actually the libsbml version you installed seems to miss some of the necessary extensions (e.g. the group extension) which are needed to write a proper sbml file. Are you working with conda? The conda libsbml package is missing the needed extension, unfortunately. I have submitted a patch to bioconda, hopefully it's available soon :)

jotech commented 3 years ago

In addition, I just renamed the issue so that it is easier to get what is the topic here, hope it is fine for you!

Coming back to your question on network complementarity, there might be two other ways worth trying by pathway analysis without the need of modeling. One thing we tried once with metagenomes is to combine different fasta files or bins into one and rerun the pathway annotation. Afterwards you can compare pathway completeness of the community vs. single organisms. Another approach could be to use the pathway hierarchy from metacyc. Here it is possible to distinguish between degradation and biosynthesis pathways. If you have one organism with an biosynthesis pathway for a specific compound and another which can degrade it, then this can indicate a potential interaction!

ntromas commented 3 years ago

Hi,

Thanks! Yes I am using Conda. The weird thing is that with the '3.0.1' version of sybilSBML, I was able to generate .xml files. I will try to reinstall gapseq, maybe without Conda env... Sounds good for the name of the issue, mine was really bad! Thanks for the suggestions, I could give a try to MetaCyc for sure. Thanks !

ntromas commented 3 years ago

When I installed gapseq without conda and try to install sybilSBML, I still have an issue: R CMD INSTALL --configure-args="--with-sbml-include=/usr/local/include/ --with-sbml-lib=/usr/local/lib/" sybilSBML_3.1.2.tar.gz hecking sbml/SBMLTypes.h presence... yes checking for sbml/SBMLTypes.h... yes checking for library containing readSBML... no configure: error: Could not link to libSBML: use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker. ERROR: configuration failed for package ‘sybilSBML’

Hopefully, there will be an easier way to install this package in the future!

Cheers,

Nico

ntromas commented 3 years ago

Sorry for the spamming but I also tried with a mac machine. I followed the advices from https://gist.github.com/dosorio/ea4baf66ee68821014d7dc6d92a48c55

I got a different error this time: ** testing if installed package can be loaded from temporary location Warning: package ‘Matrix’ was built under R version 3.6.2 Error: package or namespace load failed for ‘sybilSBML’ in dyn.load(file, DLLpath = DLLpath, ...): impossible de charger l'objet partagé '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-sybilSBML/00new/sybilSBML/libs/sybilSBML.so': dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-sybilSBML/00new/sybilSBML/libs/sybilSBML.so, 6): Symbol not found: _ASTNode_isAvogadro Referenced from: /usr/local/lib/libsbml.5.dylib Expected in: flat namespace in /usr/local/lib/libsbml.5.dylib Erreur : le chargement a échoué Exécution arrêtée ERROR: loading failed

Nico

jotech commented 3 years ago

Hi, the pull request has been merged into bioconda! Do you mind giving it a try?

conda install -c bioconda libsbml
Waschina commented 3 years ago

Just as a quick add-on: We updated the conda installation instructions, which now include also the commands for libsbml and sybilSBML installation. https://gapseq.readthedocs.io/en/latest/install.html

We hope this helps

ntromas commented 3 years ago

Hi! I just tried the installation with conda and it worked!! I am now running gapseq to see if the .xml are in the shape/structure expected. Thanks a lot for your time on this!

Nico

Waschina commented 3 years ago

I am so glad to hear that! it's due to @jotech's pull request and the bioconda-community. Let us know if you spot something in the xmls that is inconsistent with the sbml format.

jotech commented 3 years ago

great :)

ntromas commented 3 years ago

Hi, Just to tell you that I could generate models and I got .xml. I played a bit with Smetana (installing Cplex was challenging too). Thanks again for your time!

ntromas commented 3 years ago

Hi again,

Just by curiosity, is it possible to run gapseq with a minimal necessities for growth (to highlight the cooperation between members of the community). In this case, which medium is recommended? By default, I guess ALLmed.csv is used, right? Thanks for your help! Nico